Untold Stories of Equestria: Episode 1 & 2- The Great Plague
by Sparrow9642
Summary: When a strange plague that causes everypony to act the opposite of themselves corrupts 4 of the Mane Six, will Twilight be able to save her friends, Equestria, and stop the plague from corrupting all of Equestria?
1. Corruption

**Hello everypony! I am mostly famous for AATC fanfics, but since I am now a brony, I figured I'd turn an rp that a friend and I did into a fanfic, so hope you enjoy! This is my first MLP fanfic, so please leave reviews and enjoy :) This takes place after the Mane Six cure the Tree of Harmony using the elements , before the chest is opened.**

 _"_ _ **Twilight's Message"**_

Twilight peeked her eyes open to a new day in Ponyville, feeling highly confident. She stretched out her limbs, hearing a few pops from her joints then made her way out of her bed. She quietly made her way past Spike still sleeping and muttering compliments to Rarity, in his sleep. Twilight giggled from Spike's compliments, as she quietly made her way down the stairs, into the library, where she used her magic to grab a book off of one of the shelves, and place it on a table. As Twilight prepared to sit down on the chair, she overheard a loud burp from Spike, and wondered if it was a letter from Princess Celestia. It didn't take long for that question to be answered, as Spike came rushing down the stairs, carrying a scroll.

"Twilight!" yelled Spike. "You gotta hear this!"

Twilight was intrigued, yet confused at the same time.

"Slow down, Spike," said Twilight. "What does the letter say?"

Spike unrolled the scroll, and started to read.

" _My dear Twilight,"_

 _"I send this message as a warning. This morning when I raised the sun, my sister was attempting to raise the sun herself. She claimed that she had all the powers that I have, and that I was the one that raised the moon. At first, I thought it was mere accident or joke, but now, I have slowly started to believe that I am Luna. This strange phenomenon has affected everypony of Canterlot, and I fear that Ponyville might be next. Though I have no idea of what is causing this, I know that you have a better chance of figuring this out than I do. Stay in the library, because I believe it is airborne, but that's all I can determine."_

 _Be safe,_

 _Princess Celestia_

Twilight immediately panicked. "I think I'm going to have to cancel reading my book today, because we've got a major issue!"

* * *

 _ **"Rainbow Dash's Encounter"  
**_

Rainbow Dash woke up from her dream of fighting alongside Daring Do, due to her reading a Daring Do book the night before, and stretched out her limbs and wings. She looked down at Tank, still inside his shell.

"Rise and shine, Tank," said Rainbow Dash, knocking on Tank's shell with one of her hooves.

Tank popped his head out slowly, and looked at his owner, while yawning.

"We've got a long day ahead of us, Tank, and from the looks of the sky, I don't need to clear it! Awesome!"

Rainbow Dash made her way out the bedroom, grabbing Tank off the floor, into the kitchen. She grabbed an apple she had received from Applejack a few days before, and chomped it down.

"That's better, but it would be better in a cider."

Rainbow Dash grabbed another apple, and sliced a small bit from the apple, then handed it to Tank.

"Eat up, Tank," she said, holding the apple slice in front of the tortoise's mouth.

Usually, Tank wouldn't hesitate in eating the apple, but this time, Tank retreated into his shell, refusing to eat the apple. Rainbow Dash was confused.

"What's wrong, Tank?" asked Rainbow Dash.

Tank just remained in his large shell, not interacting with Rainbow Dash.

"Are you sick!? You love Applejack's apples."

Tank was silent, remaining inside of his shell.

"I know! Let's go see Fluttershy! She'll know what to do!"

Rainbow Dash grabbed Tank, and rushed out of her home, hoping that Fluttershy might have a clue of what might be wrong with Tank. Rainbow Dash didn't waste any time, and flew at full speed in the direction of Fluttershy's cabin. She arrived within a minute, already noticing something strange; all of Fluttershy's animal friends were not present, and it was dead silent.

"Something fishy is going on," said Rainbow Dash, as she knocked on Fluttershy's door. "Fluttershy, I need help. I think Tank is sick."

At first, there was no response, then the door opened, revealing Fluttershy in the doorway.

"You gotta help me!" exclaimed Rainbow Dash, noticing something funny about Fluttershy.

"Help?! How can I help!?" exclaimed Fluttershy in an angry tone. "Animals hate me! They've always hated me!"

Fluttershy slammed the door in Rainbow Dash's face, following Fluttershy locking the door.

"Something weird is happening. I need to get to Twilight," said Rainbow Dash, but as she turned to leave, she suddenly started to feel strange.

Rainbow Dash felt light-headed, and started to feel different. She started to feel very depressed, and afraid.

"What's happening to me?" muttered Rainbow Dash, as the transformation finished, and Rainbow Dash too, was corrupted.

* * *

 _ **"Fluttershy's Encounter"  
**_

" _Ten Minutes Earlier"  
_

Fluttershy fed all of her animal friends their breakfast, which was an assortment of different foods. For all the birds, she fed them normal bird seed, while for others such as Angel, she fed them salad and vegetables. Angel was being stubborn, as always, refusing to eat his food, because it didn't have a certain ingredient. Fluttershy continued to persuade Angel, as kind as she could.

"Oh, Angel, would you please eat the food," said Fluttershy. "I'm sorry, but I don't have what you want."

Angel shrugged, and shook his head. Fluttershy was offended, but she wasn't giving up.

"I made it with all my love, and you'll make me sad if you don't."

Angel retaliated by kicking over the large dish of food. Fluttershy sighed, then suddenly felt a strange urge come over her body, and even caused her to feel angry. She wondered what was wrong, but it was already too late, as she returned to her attempts to get Angel to eat.

"Well then, if you don't want this, then maybe you'll want this!" she yelled, while grabbing a nasty plate of food from the garbage can, and dumping it on Angel. "Well, go on Angel. EAT IT!"

Angel got scared, as he grabbed a handful of the gunk, and hesitated to stick it into his mouth.

"EAT IT, NOW!" yelled Fluttershy, forcefully shoving the gunk into Angel's mouth.

Angel attempted to spit out the gunk, but Fluttershy retaliated.

"Now, chew it up! You are eating this, since you couldn't accept what was given to you!"

Angel didn't argue, chewed up the nasty food, and swallowed it, starting to cry.

"Now, maybe that'll teach you to respect what you are given, and not throw a fit over it!" yelled Fluttershy. "I want every bit of this food gone, Angel, and I mean EVERY BIT OF IT!"

Angel obeyed, knowing Fluttershy was serious, and did his best to chew and swallow every bit of the nasty gunk. The rest of Fluttershy's animal friends stood, shocked that their owner was acting so relentless. Fluttershy stared at her animal friends, with an intimidating look on her face.

"What are all of you looking at!? Eat your breakfast, or would you like to join Angel?!"

All the animals jumped in fear, and returned to eating their breakfast.

"That'll teach all of you to never disobey me ever again! EVER!"

Fluttershy's cabin was dead silent for the first time ever, without a peep.

* * *

 _ **"Rarity's Encounter"**_

Rarity stood before her sewing machine, working on a fashion line for Sapphire Shores, with her younger sibling, Sweetie Belle assisting.

"Sweetie Belle, could you be a dear, and hand me the scissors," asked Rarity.

"Sure, sis. I know how important this is for you, so I'm willing to help," replied Sweetie Belle.

"I appreciate the help. This could be my chance to finally become one of the best fashionistas in Equestria, meaning it has to be perfect."

Sweetie Belle handed Rarity the scissors from a table, across the room. "Here you go, sis," said Sweetie Belle.

"Thank you, darling," replied Rarity, using her magic to grab the scissors from Sweetie Belle, and finish the final touch on the outfit. "One last cut, and done!"

"Thank goodness," said Sweetie Belle, collapsing from exhaustion. "Am I free?"

"Yes. Go play with your crusader friends. I can handle the rest," replied Rarity.

"Thanks, Rarity!" exclaimed Sweetie Belle, giving her big sister a hug.

"No. Thank you. Without your help, I may have never gotten this done in time."

Sweetie Belle smiled, then dashed out of the room.

"Alright. Now, I'd best hurry to Canterlot, so I can debut these beauties."

Using her magic, Rarity packed the outfits into a box, while wiping sweat from her forehead.

"SWEAT! I can't be sweaty now! I must be looking as fabulous as ever!"

Rarity looked around for a way to get herself to cool down, then realized she had a window.

"I suppose opening a window wouldn't hurt. If it helps to rid my body of dreaded sweat!"

Rarity opened the window, using her magic, and took in a big breath of fresh air.

"Ah. Much better."

Suddenly, Rarity started to feel funny, and had the urge to get as dirty as possible. She shook her head in an attempt to rid her thoughts of getting dirty, but it was already too late, for she had become corrupted from whatever was plaguing Equestria.

* * *

 _ **"Applejack's Encounter"**_

It was a quiet day at Sweet Apple Acres, as Applejack rose from her slumber, grabbing her hat from its hat stand. She let out a long yawn, as Apple Bloom rushed into her room, all hyped up about something.

"Well, come on, sis! We need to get to work!" commanded Apple Bloom.

"Whoa. Slow down, sugarcube," said Applejack.

"How can I?! Today we need to buck a ton of apples from the trees, for the celebration Princess Celestia is preparing for you, Twilight, Rainbow Dash, Rarity, Pinkie Pie, and Futtershy in Canterlot!"

Applejack suddenly remembered that Princess Celestia had decided to throw a celebration, due to them having the courage to save the Tree of Harmony by giving up the Elements of Harmony.

"Shoot! I totally forgot!" exclaimed Applejack. "Come on, sugarcube! We have no time to waste!"

"Right behind ya, sis!" replied Apple Bloom, rushing out of the bedroom.

Applejack rushed down the stairs, to breakfast, where she startled Granny Smith, half-asleep in her rocking chair. Granny Smith caught sight of Applejack and Apple Bloom, and stopped them before they could exit the house.

"Hold it, you two!" commanded Granny Smith.

"But, Granny Smith, there's no time! I need to get buckin' with Big Mac!" exclaimed Applejack.

"You worried too much, Applejack. I want you to eat some breakfast first, because you'll need all the energy you can get. You remember what happened last time you tried bucking all by your lonesome, right?"

Applejack started having flashbacks of her last Applebucking season, and remembered the result of it, until Twilight and the others came along and helped.

"You're right, Granny Smith, as usual," confessed Applejack.

Granny Smith smiled, while Applejack and Apple Bloom took their seats and ate their breakfast. Once Applejack and Apple Bloom finished their breakfast, they returned to their business, and rushed out the farmhouse, toward the orchard where they saw Big Macintosh sitting on the ground playing around with an apple.

"What in tarnation?" said Applejack, rushing over to Big Macintosh. "What you doing, Big Macintosh? We need to be buckin', not restin'."

Big Macintosh didn't respond and continued playing with his apple. Just as Applejack was about to get aggressive, she felt a strange feeling overcome her, and she too started to feel lazy.

"You alright, sis?" asked Apple Bloom.

Applejack didn't respond and sat down on the ground, pulled her hat over her eyes, and started to sleep.

"Not funny, Applejack! Come on! We can do this, even without Big Macintosh!"

Applejack didn't move, and continued to rest next to Big Macintosh. Apple Bloom couldn't ignore it anymore, and knew that something was wrong, so she rushed back to the farmhouse, and locked the door.

"What are ya doin', Apple Bloom?" asked Granny Smith.

"Granny, there's somethin' wrong with Applejack," replied Apple Bloom.

Granny Smith was confused. "What do ya mean?"

"Well, we walked out to the orchard, and found Big Mac on the ground, then Applejack suddenly started acting different. She just lied on the ground, and started acting lazy."

Granny Smith had heard enough. "I want you to close every window in the house, and stay inside."

"What? Do you know what's wrong with Applejack?" asked Apple Bloom.

"Yes, and I'm afraid that unless there is a pony out there that is not corrupted, we all might be in big trouble."

 **That's all for now! More is to come in the future, so don't worry, I'll try to update as fast as I can, but depending on how things go, I don't know how long it'll be! Leave reviews, follow, and favorite this for the latest update! Hope you enjoyed the opening to the first of this fanfic, and until next time, take care:)**


	2. The Source

Back at the library, Twilight scrambled through every book she could find with the assistance of Spike, hoping to find something on what was happening to not just Ponyville, but all of Equestria. Twilight used her magic to flip through the pages of the books, skimming through each page, looking for any key words , but so far, there was no such thing.

"Come on! Come on! There's gotta be something here!" she muttered to herself out of frustration.

As she scrambled through each book, small droplets of sweat fell from her forehead, and she was too stressed to notice that she was nearly hitting Spike with the books she tossed aside. Spike dodged every book, while scrambling through any book he could get his claws on, hoping to find anything. The books he was looking through were mostly based on historic events that had happened in Equestria, and were intriguing, but not at all what they were looking for.

"Find anything, Spike?" asked Twilight.

"Not a thing," replied Spike. "Only things on Equestria history."

Twilight let out a sigh of frustration, surprised that there was not a single book in her library that associated with their situation.

"What am I going to do?!" exclaimed Twilight. "Princess Celestia trusted me in finding the solution to this epidemic, but I've been through every book I own, and have absolutely nothing!"

"Calm down, Twilight," said Spike. "I'm sure we'll figure something out."

Twilight paced back and forth, feeling completely helpless, until there was a knock at her door. Twilight didn't want to risk any chance of becoming corrupted, but she wondered if it could be one of her friends.

"I'll just have to be quick," she said to herself, as she paced toward the door, and unlocked every lock on the door. She quickly opened the door, only to see Pinkie Pie with her breath held. Her face was purple from lack of oxygen, so Twilight used her magic to lift Pinkie through the doorway, and shut the door.

Pinkie let in a huge breath of air, knowing she was safe from the epidemic. "Twilight! You gotta help me! All the people in Ponyville are acting crazy from something strange in the air! Nobody's even smiling!" exclaimed Pinkie Pie.

"I'm aware, Pinkie," replied Twilight. "I've been trying to find a cure, but there is nothing in my library that can help. I think I've been _stumped_."

"Is that why you're all "down in the dumps?" asked Pinkie Pie.

"Is it really that obvious?" replied Twilight.

"Absolutely, but you can't give up so easy! So what if the answer is not here? Sometimes a solution doesn't lie in text, but within yourself!"

Twilight thought about what Pinkie said, and realized that she was right.

"You're right, Pinkie!" exclaimed Twilight. "Maybe I'm just not looking in the right place for the answer to my problem!"

"That's the spirit!" replied Pinkie Pie.

"Only one problem; the solution lies in the Castle of the Two Sisters, which is wide open to air."

"Oh, come on, Twilight! You must know a spell of some sort that can prevent you from being exposed to the air!"

Twilight thought for a second, then remembered the spell Cadance cast to prevent her from catching Discord's supposed flu. "I guess I can try to alter a spell Cadance used to protect me from Discord's flu, so that it keeps the toxin in the air out."

"Great idea, Twilight!" said Pinkie Pie. "That's perfect!"

"However, if I mess up even the smallest bit on the spell, you know what happens then, so I suggest you take a deep breath, Pinkie," warned Twilight. "I have no idea if this is going to work or not."

Pinkie gulped at the sound of Twilight's words, along with Spike.

"You can do it, Twilight!" encouraged Spike. "You represent the Element of Magic, so this should be cake!"

"Thanks, Spike," replied Twilight as she prepared the spell. "Well, here goes nothing."

Twilight's horn glew with a hue of purple, as she pushed all her effort into the spell, and finished the spell, with all three of them being enclosed in an invisible dome of magic. The only problem was that Twilight had to keep using all of her strength, in order to keep the spell's alternations in tact.

"You okay, Twilight?" asked Spike.

"Yeah," replied Twilight. "This is just a powerful spell, and I have to put a ton of strength into it, unlike other spells."

Twilight struggled, as she made her way toward the door. "Take a deep breath, you two, because I don't know if this is going to work or not," she said, opening the door. "Brace yourselves!"

All three of them made their way to the outside of the library, where it was quiet, and every pony seemed depressed and sad, when it was just the effects of what ever was causing Equestria to turn topsy turvy. Twilight looked around for any of her other friends, hoping not to see them corrupted as well. Fortunately, she didn't see any of her friends, but was still horrified at the sight of Ponyville. She took a deep breath, so she could test if her spell had worked, bracing for the worst outcome.

Twilight didn't feel any sort of change inside of her, and was happy that her spell had worked.

"It worked!" exclaimed Twilight. "Now, if I can just keep this spell going, I think that we'll be okay."

"Thank goodness," said Spike, relieved that Twilight's spell had worked.

"Come on! We've got to get to the Castle of the Two Sisters!" commanded Twilight. "I just hope I can last that long, before my magic resources run out of juice."

"Sure you can!" encouraged Pinkie Pie.

"Right," replied Twilight, as she hurried in the direction of the Everfree Forest.

* * *

Twilight and the others managed to make to the Everfree Forest without any troubles, while noticing something else about the Everfree Forest. There was a large cloud of smoke coming from the center of the forest, which immediately made Twilight wonder if this could have something to do with what was going on throughout Equestria.

"A mushroom cloud!" exclaimed Pinkie Pie. "Maybe, there's a party going on in the Everfree Forest!"

"I don't think so, Pinkie," said Twilight. "This could be the answer to our problems."

"Then I guess I won't be needing this," replied Pinkie Pie, tossing her party cannon into a nearby bush.

Twilight studied the smoke cloud closer, estimating where it could possibly be coming from. Once she finished studying the smoke cloud, her heart sunk. "That's coming from Zecora's! Come on! We need to help her!"

Twilight, along with Spike and Pinkie trotted into the forest, toward Zecora's hut, where Twilight's estimation was correct. A strange smoke was coming from the chimney of Zecora's hut, and even out of every other opening of the small hut. Twilight feared that her magic wouldn't be able to withstand a mirage of the smoke, but Zecora was her friend, and she wasn't going to just abandon her.

Twilight gulped, as she approached Zecora's door, and opened it, only to be nearly blown away by a large amount of the strange smoke, almost losing control of her spell. Once the smoke was clear, Twilight entered the hut, hoping to find Zecora safe and sound, but strangely, there was no sign of Zecora.

"Zecora!" yelled Twilight, still looking around for her.

There was no sign of her, but Twilight noticed something else; the cauldron where Zecora mixes her remedies was erupting large amounts of the smoke from before. The brew was a putrid color, and looked as if it were sick.

"What do you think Zecora is making?" asked Spike.

"I have no idea, Spike," replied Twilight. "This brew doesn't even look right, as if it's rotten."

Out of nowhere, a familiar voice spoke. "Indeed, you are right, my dearest friend, Twilight."

Twilight turned around, only to see Zecora standing.

"What the hay!?" exclaimed Pinkie Pie. "How are you not corrupted by your own creation?! Are you _magic_?"

"Relax, dear friend. For this outcome, I did not intend," said Zecora.

"But, Pinkie does have a good point," said Twilight. "Why are you unaffected, while the rest of Equestia is acting crazy?"

"The reason I do not know, only that if not stopped, my brew will continue to grow," replied Zecora.

Twilight knew Zecora was right, and that now was not the time for speculation and judgement.

"How do we stop it then?" asked Twilight.

"Listen closely to what I say; the cure is not too faraway. Deep in the Everfree Forest, there is an ancient flower, but beware! It won't be easy to obtain it's power. Free your friends from their corruption, only then, will you be able to save Equestria, once again."

"What plant is it, and where can we find it, Zecora," asked Twilight.

Zecora grabbed an old book off of one of her tables, and opened it to a page, showing Twilight the plant.

"The Everfree Lotus," said Twilight. "Good. I know what we need to do. First step; gather the others and free them of their corruption."

 **END OF EPISODE ONE**

 **You don't know how much of a pain Zecora is to do! Will Twilight be able to free the others of their corruption, and just what is the Everfree Lotus? Keep an eye out, because the next chapter might be up soon Thanks for reading!**


	3. Pony Wrap Up

Twilight, Spike, and Pinkie set out to find the other corrupted Mane Six, and with the help of Zecora, were given seven magical charms, and were able to wander throughout Ponyville without Twilight's spell protecting them, thanks to the help of the charms that provide protection from negative forces. Zecora had to stay behind, so she could keep her brew from spiralling out of control, but Twilight and the others would have to hurry, because the brew was getting stronger by every second.

Twilight thought of where she would be able to find her friends, now corrupted, and had to think outside of the box, seeing they were the opposite of themselves now. Normally, Rainbow could be found sleeping on a cloud above Ponyville, but since she was the opposite of herself, that was most unlikely.

"Any ideas of where we could find Rainbow?" asked Twilight.

"Well, seeing she's the complete opposite of herself, she wouldn't be flying," said Spike.

"I'm aware of that, Spike, so we need to think of where she'd be."

"Well, in order to do that," said Pinkie. "We need to think of Rainbow Dash differently."

Twilight smiled at Pinkie's suggestion, knowing she was right, so Twilight started to evaluate Rainbow's personality, in her mind.

"Let's see. Rainbow is normally confident, athletic, and fearless," evaluated Twilight. "So, the opposite would be she's cowardly, lazy, and afraid of everything. Even her own shadow."

"Sounds a little like Fluttershy," confirmed Spike.

Twilight want to facehoof herself, realizing Spike had nailed it.

"Spike, you are a genius!" exclaimed Twilight.

"I am?" questioned Spike.

"Come on. Let's exclude finding Rainbow, and focus on Fluttershy, first, and I have an idea of where she is," said Twilight.

Pinkie and Spike didn't question Twilight, seeing she was one of the smartest ponies in all of Equestria, and just followed her lead.

* * *

Twilight led all three of them to Fluttershy's cottage, just along the outskirts of the Everfree Forest, where the smoke cloud was visible. The smoke cloud was starting to darken and increase in size, so none of them wasted any time, and rushed across the bridge, toward Fluttershy's cottage, which they noticed was quiet.

"My suspicions were correct," said Twilight, noticing a white ball of fur climbing out of one of Fluttershy's open windows, which she identified as Angel.

He looked sick and very afraid, so Twilight called out to him, only to have him dash over to her, and hug her left-front leg. She could tell from the pressure of the hug that Angel was in desperation.

"What happened, Angel?" asked Twilight.

Angel acted out what had happened, similar to a game of charades, and Twilight recognized every action.

"Don't worry, Angel," said Twilight. "We'll have Fluttershy back to normal in no time."

Twilight, along with Spike and Pinkie approached Fluttershy's cottage door, and knocked on the door. Fluttershy responded from behind the door, and it even frightened the three of them a little.

"GO AWAY! EVERYPONY HATES ME!" yelled Fluttershy.

"Fluttershy, you're corrupted, and if you don't open the door, I'll force it open," said Twilight.

"FLUTTERSHY MAKES ALL THE ANIMALS CRY!" responded Fluttershy.

Twilight knew that Fluttershy wasn't going to reason, so she used her magic to force open the door, revealing a corrupted Fluttershy with piercing red eyes sitting in the middle of the cottage.

"I told you to LEAVE ME ALONE!" yelled Fluttershy.

"Not happening," assured Twilight, approaching Fluttershy.

"STAY AWAY!" commanded Fluttershy.

Twilight ignored Fluttershy's commands, and continued to approach her. In response, Fluttershy dashed upward, using her wings to fly.

"Can't catch me up here!" said Fluttershy.

"Oh really?" replied Twilight as she spread her wings.

"Oh for Celestia's sake!" exclaimed Fluttershy, as she dashed away from Twilight in full pursuit of her.

Twilight was still new to flying, despite Rainbow giving her flying lessons, so she was nowhere close to as fast as Fluttershy. As much as she didn't want to harm a friend, she started firing beams of magic from her horn, in an attempt to slow down Fluttershy. After nearly two minutes of flying, Twilight fired a beam from her horn and managed to hit Fluttershy's right wing, immediately causing her to fall.

"Pinkie! Spike! Catch her!" yelled Twilight.

Pinkie and Spike hurried to catch Fluttershy, but were too slow to even make it to her position. Just as Fluttershy was about to hit the hard floor, Harry, her pet bear grabbed her in his paws. The corrupted Fluttershy looked up at Harry, surprised that after all she had done, he had still saved her from injury.

"But, I thought you hated me?" said Fluttershy.

Harry shook his head, gesturing a "no," and already, Fluttershy was starting to change, but not completely. All her animal friends came out of hiding to comfort Fluttershy, even Angel who hopped onto her expressing a smile.

"Gosh, and here I thought I was hated by all of you, but now I realize that friendship is more powerful than what ever caused me to act so ruthless," she said in her low tone voice.

Twilight landed, wiping sweat from her forehead, and approached Fluttershy slowly.

"I'm sorry I had to do that, Fluttershy, but it was the only way I could weaken you long enough for me to free you of the corruption that is plaguing you," confessed Twilight.

"It's alright, Twilight," replied Fluttershy. "If I am corrupted like you say, then do whatever you need to do to free me of it. I'd rather be somepony full of kindness, rather than a ruthless pony."

Twilight nodded her head, then charged up her horn with the spell she used to free everypony of Discord's corruption. She placed her horn against Fluttershy's forehead, and cast it, freeing Fluttershy of her corruption.

Fluttershy came back to her senses, and looked around, confused on what had just happened.

"What happened?" asked Fluttershy.

"I'll explain later," replied Twilight. "For now, take this charm. It'll protect you from being corrupted again."

Fluttershy took the charm from Twilight, and stuck it somewhere safe.

"One down, three to go," said Spike.

"Goodness, what is this trash doing all over the floor?" said Fluttershy.

Angel acted out what she had done to him, and she immediately gasped.

"Oh dear! I'm so sorry, Angel. Tell ya what, later I'll make you a nice snack. It's the least I can do after feeding you garbage."

Angel agreed, following Twilight questioning Fluttershy further.

"Fluttershy, I need to know if you've seen Rainbow Dash at all today," asked Twilight.

"I haven't, unfortunately," replied Fluttershy.

Twilight sighed, before she suddenly spotted Tank near the front doorway.

"Strange," said Twilight. "If Tank is here, then Rainbow must be near.

Tank didn't look good, which caused Fluttershy to act.

"Oh my. Tank doesn't look good," assured Fluttershy.

"Ask him if he knows where Rainbow is," said Spike.

Fluttershy used her animal-communication skill, catching everything Tank was saying.

"He says that Rainbow Dash is hiding in the bush on the right side of the bridge, and that she brought him here earlier," said Fluttershy. "He also says that he doesn't feel well. Luckily, I know the cure for that."

Fluttershy walked into her kitchen of many animal foods, and grabbed a special food from a cabinet. She poured some of it into a small dish, and handed it to Tank.

"A bowl of this will cure that small fever, Tank," said Fluttershy.

Tank did as she said, and started munching on the food.

"Fluttershy, I hate to interrupt, but I need you to come with us, so we can retrieve Rainbow, Rarity, and Applejack," said Twilight. "We need to retrieve a special plant from the Everfree Forest, in order to free Equestria of this plague, which is just a brew gone wrong, because of Zecora ."

"T-The Everf-f-free Forest?!" exclaimed Fluttershy.

"Yes, and we need you," replied Twilight.

"Uh, today is not a good day. How about next year?"

"Looks like we're going to have to do this the hard way," said Twilight, grabbing Fluttershy's tail, and dragging her out of the cottage.

"Why me?!" exclaimed Fluttershy, as she exited the cottage.

Angel and the others, barricaded the front door to the cottage, so Fluttershy couldn't run home, while Twilight made her way to the bush that Rainbow Dash was hiding in. Twilight wasted no time, and used her magic to force Rainbow out of her hiding spot.

"NO! I don't like the thing that follows me everywhere!" exclaimed Rainbow Dash, in a similar position to Fluttershy when she is scared of something.

"Guys, I need you to hold her down, while I cast the spell on her," commanded Twilight, as Pinkie, Spike, and Fluttershy held Rainbow down.

Twilight charged up another spell, and quickly cast it on Rainbow, immediately coming back to herself.

"W-What happened? asked Rainbow Dash.

"No time to explain. Just take this charm. It'll protect you from what caused you to become corrupted," replied Twilight.

Rainbow accepted the charm, and stuck it around her neck.

"Two to go. Now, where would we find a Rarity that is the opposite of herself?" thought Twilight, immediately coming up with a solution to where Rarity would be; Sweet Apple Acres.

* * *

Spike and the others were confused why Twilight would think Rarity would be at Sweet Apple Acres of all places, but didn't argue with Twilight, because she had been right so far about everything, so there was no room for argument. The three managed to make it to Sweet Apple Acres quick, due to time running out for Equestria. All five of them wasted no time, and rushed to the mud pits, where they found Rarity rolling around in mud, dressed in a silly outfit.

Rainbow busted out laughing at the fact of Rarity getting dirty, catching Rarity's attention.

"Howdy, y'all! Would you care to join me?" suggested Rarity.

Twilight rolled her eyes, and cast the spell on Rarity while she was still distracted. Rarity shook her head, wondering where she was.

"Where am I? asked Rarity. "HUH!? What am I doing in this dreaded mud?! What sort of atrocity am I dressed in?! What has gotten into me?!"

"I'll explain later, Rarity," said Twilight. "Take this charm, otherwise you'll be rolling in mud again."

Rarity gasped, and quickly grabbed the charm from Twilight, and placed it around her neck.

"I believe that this charm could use some rubies, but I suppose it'll have to do for now," said Rarity.

Everypony laughed. "Alright. One more pony left; Applejack," said Twilight.

"You don't have to look far for her, darling," said Rarity. "She's right there, in the orchard."

Twilight looked toward the orchard, and spotted both Applejack and Big Macintosh resting under a shady apple tree.

"Good eye, Rarity," said Twilight.

"I'm fabulous, as always, dear," replied Rarity.

Twilight wasted no time, and quickly rushed to where Applejack was resting, and cast the spell, not giving Applejack any chance to respond. After the spell was cast, Applejack stood up.

"What happened?" said Applejack.

"I'll explain later, Applejack," said Twilight. "Take this charm, otherwise you'll end up like Big Macintosh."

Applejack accepted the charm, and placed it around her neck, not asking any questions.

"Well, everypony is back to normal, now we just have one final task to complete," said Twilight. "Come on, everypony. We're going into the Everfree Forest to get the Everfree Lotus."

"The Everfree what?" asked Applejack.

"Just trust me, Applejack. All will become clear when we get to our destination."

"Which is?"

"Dragon's Trench, the only place where the Everfree Lotus is said to grow."

Everypony gulped, as they made their way toward the Everfree Forest.

 **Will the Mane Six be able to obtain the Everfree Lotus? If so, will they be able to save Equestria from Zecora's brew, and why is the destination called "Dragon's" Trench? Poor Fluttershy Next and final chapter will be up soon, so leave comments, and thanks for reading.**


	4. The Dragon's Test

All of the Mane Six marched forward, into the Everfree Forest, which seemed less scary than usual for some reason. Even Fluttershy found the Everfree Forest less frightening, and more of a welcoming environment to everypony, which is an uncommon thing, seeing Rainbow had to literally drag Fluttershy just to get to the Everfree Forest.

"What the hay is going on here?" asked Applejack.

"Yeah. Fluttershy is usually afraid of the Everfree Forest, but now she's all find and dandy with it," added Rainbow Dash.

"I'm not sure, girls," answered Twilight. "I guess that Zecora's brew has become powerful enough to corrupt more than just ponies now."

"So, you're saying Zecora's brew has gained the power to corrupt an entire forest!?" exclaimed Rainbow Dash.

"Well, yes," replied Twilight.

"This is bad! Really, really bad!" shrieked Rainbow Dash. "This is starting to seem like a Daring Do book I just read last night, where Daring Do has to enter an unknown environment that's been changed by Ahuizotl, using some newly-obtained evil magic. It was epic!"

"Focus, Rainbow!" snapped Twilight.

"Hehe. Sorry, Twilight."

"I don't mind this change the slightest," said Rarity. "I think it fits the forest marvelously."

"Me either," said Fluttershy. "It's not dark and scary anymore, making me feel more comfortable."

Twilight sighed, then continued into the Everfree Forest, which had been turned into a fun house.

* * *

Everypony proceeded deeper into the Everfree Forest, deeper than they had ever gone before, noticing that the Everfree Forest had again started to change, only this time it wasn't back to a scary or fun environment, but more of a spiritual environment, as if they had wandered into a different dimension. Everypony started to feel strange, and unwelcome at the same time.

"It it me, or does it seem like I'm starting to feel a bit queezy?" said Applejack.

"Not just that, but much heavier too," said Rainbow Dash. "I can barely keep myself flying."

"Perhaps you should join the rest of us, instead of straining yourself, Rainbow," suggested Twilight.

"No thanks," said Rainbow Dash. "This is perfect exercise for my wings, especially if Cloudsdale ever accidentally starts a severe storm."

"Suit yourself," replied Twilight, seeing Rainbow struggle.

As they continued walking, the gravity of the area seemed to get heavier by the second, eventually causing Rainbow to collapse to the ground.

"Come on, Rainbow Dash!" exclaimed Rainbow, struggling to get up from the ground.

Everypony else was struggling to even stay on their hooves, feeling as if the sky was forcing them to the ground, but with much effort they were able to stay standing, especially Applejack, seeing she was the most fit pony still on her hooves.

"My stars, what is happening to us?" said Rarity.

"Care to explain, Twilight?" said Applejack.

Twilight didn't know how to respond, because she was unsure of what exactly was happening.

"I don't know what is going on, and had no idea this was even going to happen," said Twilight.

"Well, depending on how much further we have to go to this, Dragon's Trench, I'm not sure if I'm going to even be able to make it, sugar cube," said Applejack.

"How am I supposed to even go anywhere?!" snapped Rainbow Dash, still trying to lift herself from the ground.

"Use your "rainbow" strength, silly!" joked Pinkie Pie.

"Not the right time for jokes, Pinkie," replied Rainbow Dash.

"This is absurd! How are we supposed to continue when we can barely stand on our hooves, and one of us is down for the count?!" Rarity snapped.

"Keep trying, girls, otherwise, Equestria is doomed," said Twilight, trying to keep everypony together.

"Can't you just do a spell that would make this less difficult, Twi?" asked Applejack.

Twilight was unsure if she even knew a spell that could do such a thing, but she decided to think hard about it, due to her reaching her breaking point as well. The heaviness made it hard for her to even think straight, so she couldn't think of any solution, and was only mere seconds from giving up, until she suddenly felt the heaviness fade away.

"What the?" questioned Twilight.

The other six stood high on their hooves, including Rainbow Dash who had lifted herself from the ground.

"That's more like it!" said Rainbow Dash. "Thanks, Twilight! Whatever you just did helped alot!"

"Uh, sure, Rainbow," replied Twilight, confused on what just happened.

"What's wrong, darling?" asked Rarity.

"Oh. Nothing. I guess I'm just a bit exhausted from all that's happened today, that's all," replied Twilight.

"Aren't we all, darling?"

"Well, let's go get this Everfree Lotus or whatever it is, so we can all save Equestria, and laugh about it later," commanded Rainbow Dash, dashing forward, past a bunch of crystalized trees.

"Right. Let's get to it!" agreed Rarity, dashing forward.

As Rainbow and Rarity continued onward, Twilight just stood, confused in her stance.

"You alright, sugar cube?" asked Applejack.

"I'm fine, Applejack. Let's catch up, before those two encounter something in this forest," concluded Twilight.

"Alright. If you say you're good, then I guess that's fine with me," said Applejack, while continuing further into the forest.

Pinkie and Fluttershy followed, as Twilight and Applejack moved past the thickest parts of the forest. Rarity and Rainbow decided to take their time as well, unaware of whatever may wander in this part of the Everfree Forest, if they were even in the Everfree Forest anymore. The trees were coated in a crystal-like bark, and glimmered like diamonds and gems. Spike had even started to drool a little from the sight, but due to Twilight being present, he didn't dare to even try eating the bark, even though it looked scrumptious to him.

Rarity was also mesmerized by the sight, and was even tempted to take some of the bark for her boutique, but she knew that they already had enough problems to deal with at the moment, and didn't want to start anymore problems by stealing something so beautiful and sacred. She did her best not to even look at the bark, but that was pretty hard to do, seeing the bark was coated on every tree, and there were trees everywhere. She wanted to cry over how beautiful the bark was, but somehow kept herself focused on the task at hand, which was retrieving the Everfree Lotus.

After walking past the thickest pasture of the forest, the trail came to a small opening, with a gigantic trench at the end, which could only mean that they had finally reached Dragon's Trench. Twilight decided take the first steps toward the trench, seeing she had wings, and was a decent flier. She approached the edge of the bottomless trench, only to see a large group of sparkling flowers growing from the sides of the trench, in the deeper regions.

Twilight immediately recognized the flower as the Everfree Lotus, which was a black flower with pedals covered with crystal shards, and a blue stem. The Everfree Lotus was said to have been created as a fluke in one of Princess Celestia and Luna's sun and moon rises. The sun and moon were raised at the wrong times when Celestia and Luna were younger, still trying to adapt to their new-found abilities, and the alternation in time with the sun and moon created a strange reaction in the soils of Equestria.

The soils of Equestria became infested with a crystal-like fungus, and spread all throughout Equestria. To stop the fungus from spreading any further, Luna and Celestia used their magic to rid away the fungus, and as a result of magic infusing the fungus, the Everfree Lotus sprouted from the grounds of the Castle of the Two Sisters, and was used as a substitute for many things, including medicines to cure incurable diseases. However, the Everfree Lotus became abused, and was removed from anypony's reach, to a place that only the two sisters could access at will, which came to be known as Dragon's Trench.

"It's here!" exclaimed Twilight. "The Everfree Lotus is here!"

"Well, what are you waiting for?" asked Rainbow Dash. "Swoop down and grab one, so we can save Equestria."

Twilight nodded her head, then spread her wings, so she could retrieve one of the Everfree Lotus's, but was stopped when she heard a roaring sound coming from deep within the trench. That's when it dawned on Twilight why it was called "Dragon's" Trench, and shook in terror as a giant dragon sprouted from the trench. Twilight gulped, awaiting whatever the dragon had in store for her.

* * *

The dragon peeped its eyes open and looked at Twilight with large amounts of curiosity, but Twilight couldn't tell if the dragon was angry or not, due to it's ancient face having no expression at all.

"Greetings, Mr. Dragon. My name is...

She was immediately cut off by the ancient dragon.

"SILENCE!" yelled the dragon. "Why have you come here, and for what reason?!"

"My name is Twilight Sparkle, and I'm a former student of one of the pony's that created you," spoke Twilight, trying to keep herself as calm as possible. "You probably know her best as, "Celestia."

"Celestia created the side of me that is full of all that is "good," young one. She created me to protect what you seek, and I see that you are telling the truth about being her former student," said the dragon.

"How can you tell?" asked Twilight.

"The two sister's magic gives me the power to do many things. Celestia gives me the power to see the good in a pony's being, while Luna's gives me the power to see the bad in a pony's being," answered the dragon.

"I see. The sun ables you to see all good, while the moon ables you to see all bad."

"Exactly, young one. You are a smart subject, and that is good. I also see that you use your gifts for good too."

"Mr. Dragon, I don't mean to be pushy, but Equestria is in great trouble, and we need the Everfree Lotus to save it."

"Only those of great importance are allowed to possess the lotus," claimed the dragon. "It must also be only for a dire situation."

"Trust me. This is a very dire situation."

"I see that it is, but the other subjects with you must be of great importance as well, young one."

"Oh. No need to worry about that," said Twilight. "My friends are of much great importance, because they each represent one of the Elements of Harmony."

"I'll be the judge of that," said the dragon. "If they are of true importance, they will come forth, and stand before me while I examine their souls. If they are worthy, I shall grant you the lotus. If they're not, then I shall burn each them into another dimension."

Twilight gulped. "Fair enough. Rainbow! Fluttershy! Rarity! Pinkie! Applejack! Do as the dragon says, otherwise we came here for nothing!" assured Twilight.

"Alright, Twi," said Applejack. "We're comin' out."

As promised, all five of them proceeded out of the trees, with Rainbow dragging Fluttershy by her tail.

"I sense one other subject. Who are they?" asked the dragon.

"That would be my loyal assistant, Spike. He's a dragon, just like you, and has a connection to Celestia too," confirmed Twilight.

"Fair enough. I sense no evil in this " _Spike's_ " heart, so I'll make an exception."

Twilight let out a breath of relief, but it was far from over, because now her best friends had to pass the dragon's test. The dragon overlooked the other five with much curiosity, reading each of their hearts and souls. Twilight was literally holding her breath in suspense, and as the dragon started to speak, she started to sweat a little bit.

"There is much in each of your hearts. I sense large amounts of laughter, kindness, loyalty, generosity, and honesty. Each representing an Element of Harmony," said the dragon. "You have been through much conflict, but have overcame it with the magic of friendship, and no matter how hard times have gotten, you've always stood up for one another, even in the darkest times. Your bond is strong, and you have yet to accomplish much more in your lives. You are worthy of the lotus, fellow ponies."

The dragon reached down into the trench, pulled an Everfree Lotus from the trench wall, and handed it to Twilight.

"Good luck, everypony. May you have a safe journey," said the dragon, as he dove back into the trench.

As Twilight held the lotus, she could feel the power of both Celestia and Luna inside the plant, as it sparkled in the sunlight. It was a power she had never felt before.

"You alright, Twi?" asked Applejack.

Twilight shook her head, until she came out of her daze. "I'm fine. Now, let's go save Equestria!"

"Right!" said everypony in unison, as they made their way back in the direction of Zecora's hut.

* * *

By the time the Mane Six, along with Spike made it to Zecora's hut, the hut was on the verge of nearly exploding.

"Come on, guys! There's no time to waste!" commanded Twilight.

All seven of them rushed into Zecora's hut, where Zecora stood exhausted from keeping the brew tamed for hours.

"Zecora!" yelled Twilight. "We've got the Everfree Lotus!"

Zecora looked at Twilight, nearly on the verge of collapsing. "There's no time to waste, my friend! Toss the lotus into the brew, so this plague can end!" exclaimed Zecora.

Twilight wasted no time, and placed the Everfree Lotus into the brew, immediately noticing the brew starting to calm, and the smoke starting to disipate.

"Please tell me it's over!" said Rainbow Dash.

Zecora nodded her head, as she collapsed to the floor.

"Phew. I've had enough adventures for one day."

"You think you have?" said Applejack. "I think we all have."

Twilight had noticed that Zecora's brew had turned a light pink color, and smelled delightful.

"Mmm, that smells delicious, Zecora," said Twilight.

"What exactly were you making, darling?" asked Rarity.

"My friends, I think I know the reason why, in the first place, why my brew went all awry. Plants from the forest, you see, need to be fresh, to create a fresh remedy. I believe I chose a rotten ingredient from a tree, and for my mistake, I truly am sorry." apologized Zecora.

"Apology accepted, Zecora," said Twilight.

"Yeah. Everypony makes mistakes, sugar cube," said Applejack.

"We understand, darling," said Rarity.

"As long as this never happens again, I guess we're cool," claimed Rainbow Dash.

"I really hope this never happens again," added Fluttershy.

Zecora nodded her head, as a thanks to the Mane Six.

"So, is this brew how we cure all of those corrupted by the previous brew?" asked Twilight.

Zecora nodded her head again, meaning the Mane Six still had one last task, before they could call it a day; they still had to cure everypony corrupted.

"Let's get to it then," said Twilight.

* * *

It took a great amount of time to cure everypony of their corruption, but luckily, there was enough of Zecora's brew to cure all of those corrupted. The brew had only managed to make it as far as Canterlot and Ponyville, lucky for the Mane Six. However, the only pony of the princesses not corrupted was Cadance, due to her being in the Crystal Empire, watching over the crystal ponies. Twilight was relieved that her stepsister was not a victim of Zecora's plague, due to her already seeing a preview of what she'd be like corrupted, courtesy of Queen Chrysalis.

After curing everypony of their corruption, Twilight and the others still had one thing to await, and that was Celestia's celebration for saving Equestria from not just the Tree of Harmony, but from the Plague of Equestria. Rarity had designed all six of them a set of outfits for the occasion, symbolizing all of their courage in overcoming all the challenges that they had faced in their pasts. Part of the inspiration came from the words of the dragon they had faced, and the beauty of the forest, along with modifications to the outfits that she had prepared with Sweetie Belle's assistance. Rarity had managed to display the outifits to Sapphire Shores, and as she predicted, Sapphire loved them.

As for Applejack, she had managed to gather enough apples for the celebration, along with the help of her friends and Big Macintosh. The apples were soaked in Zecora's brew, just in case they had been tainted during the time of the plague, due to it having the power to change an entire forest into a fun house. In the end, all the apples were gathered for the celebration and taken to Canterlot, where Celestia helped Applejack display them.

Rainbow Dash was able to rid the sky air of all the toxic smoke from Zecora's brew, and gathered all of it into a large containment device, thanks to the efforts of the Cloudsdale factory. The device was taken to somewhere afar, where nopony would ever discover it, and sealed with a lid that only Cloudsdale ponies could open, so there was no chance of the toxic smoke escaping and plaguing Equestria ever again. Even if it was, the Mane Six could just return to Dragon's Trench, gather up a new lotus, and have Zecora cook up a brew that would free a pony of their corruption, but that was most unlikely.

As for Twilight, she managed to finish the book she had started to read the morning the plague first began, which turned out to be the book that contained all the information on the Everfree Lotus that she needed in the first place. Once she had finished it, she sat it in a nearby area where she could always find it, just in case this ever happened again, but she knew that if it ever did, it wouldn't be for a long time. In other words, she knew that Equestria was safe once again, but one mystery still was unsolved; what caused the weight of the gravity to be lifted, when she didn't do anything? She didn't worry about it too much, and prepared for the celebration.

* * *

Twilight, along with her friends arrived at Canterlot Castle, exiting the carriage. All six proceeded into the castle, where they were greeted by Princess Celestia, Luna, and surprisingly, Cadance as well. Twilight was thrilled that Cadance was there, and walked up to her.

"Sunshine, sunshine! Ladybugs awake! Clap your hooves, and do a little shake!" sang Cadance and Twilight in unison.

"It's so good to see you!" exclaimed Twilight, full of excitment.

"It's good to see you too," replied Cadance.

"But, if you're here, then who's watching over the Crystal Empire?" asked Twilight.

"Shining Armor insisted for me to come, because nothing really happens in the Crystal Empire anymore, ever since King Sombra was defeated."

"I can understand why," said Twilight.

"So, I heard that all six of you had to save Equestria again. Must've been a chore."

"In no doubt. It took nearly a week just to get Ponyville and Canterlot back to normal."

"Yep, it was some adventure," added Applejack.

Cadance giggled. "I'm sure it was."

"However, I'm still unsure of one thing," said Twilight. "We were all being crushed by the gravity of the area, then like magic, we were back to normal."

"You mean it wasn't you who caused the gravity to become less heavy?" asked Rainbow Dash.

"No. I'm not sure what happened, Rainbow," confessed Twilight.

Cadance looked at them strangely. "Wait. You six were in trouble, and needed help?"

"Yeah. Why?" asked Twilight.

"Well, I was surveying the Crystal Empire, when I saw something in the distance, and strangely, it looked just like Twilight's cutie mark. I swore I could hear you six struggling, and asking for help, so I cast a spell that helps to lessen the weight of gravity. Is that even possible?"

Twilight and the others were blown away, and wondered themselves if that was even possible, but at the same time they were just happy that Cadance was able to to sense them needing help, even if it was miles away from the Crystal Empire.

"That just goes to show ya just how powerful friendship can be," said Applejack.

"That's right, Applejack. We've been through so much that we've all developed a bond that allows us to help each other, even if we are far away from one another. Friendship is the most powerful type of magic, because it lasts forever, and as long as we have each other, it will never die," said Twilight, as all six of them gathered in a group hug.

"Now, come on!" exclaimed Rainbow Dash. "Let's party!"

"Right. I could use a party, after all that's happened," said Applejack.

"My hooves could use a rest," said Rarity.

"I don't mind, as long as there's nothing scary," said Fluttershy

"PARTY TIME!" exclaimed Pinkie.

All six of them proceeded into the castle, along with Cadance, planning to catch up with Twilight. Luna and Celestia remained outside, for a quick chat.

"Sister, do you think she's ready yet?" asked Luna.

"Not yet, dear sister," replied Celestia. "Not yet. But, soon she will be ready to have her own kingdom when the time is right."

Luna nodded her head, as she raised the moon, for the day's end.

 **END OF EPISODE TWO**

 **Thanks for reading! Episode three is coming soon, so keep an eye out!**


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